phsc.plot.phy.selected.individuals: Plot short read phylogenies and highlight individuals

In olli0601/Phyloscanner.R.utilities:

Plot short read phylogenies and highlight individuals

Description

This function plots short read phylogenies and highlights the clades of two individuals in red and blue.

Usage

phsc.plot.phy.selected.individuals(
  phs,
  dfs,
  ids,
  plot.cols = rainbow(length(ids)),
  plot.file = NA,
  group.redo = FALSE,
  drop.less.than.n.ids = 2,
  drop.blacklisted = FALSE,
  pdf.h = 50,
  pdf.rw = 10,
  pdf.ntrees = 20,
  pdf.title.size = 40
)

Arguments

phs	List of trees in ape format
dfs	data.table with mandatory column 'IDX' and optional column 'TITLE'. IDX is the index of all phylogenies in 'phs' that are to be plotted. TITLE is a title for each sub-plot, for example specifying a window.
ids	Vector of regular expressions that identify individuals to be highlighted in colour.
plot.cols	Vector of colours for each individual
plot.file	If not missing, the phylogenies will be printed to file.
group.redo	Logical, indicating if the colour groups should be recalculated from ids.
drop.blacklisted	Logical, indicating if all blacklisted taxa should be dropped prior to plotting.
pdf.h	Height of the pdf file in inches.
pdf.rw	Relative width of the pdf file, internally multiplied by the number of phylogenies to give the total width in inches.
pdf.ntrees	Number of trees per pdf.
pdf.title.size	Size of pdf title in inches.

Value

List of ggtree objects, ready for printing.

olli0601/Phyloscanner.R.utilities documentation built on April 16, 2024, 5:44 a.m.